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新型コロナウイルスの構造情報

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コロナウイルス
コロナウイルス, 2020. David S. Goodsell@RCSB PDB による原画を修正

最近、新型コロナウイルス感染症(Novel Coronavirus disease 2019: COVID-19)の拡大が世界中で深刻な問題となっています。早急にこの新型ウイルス(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)を理解し有効な薬を開発するため,関連するタンパク質の構造研究は既に始まっています。そして,解明された構造はPDBに登録されていっています。PDBjでは利用者の利便を図るため,新型コロナウイルス特集ページを作成しました。新たなエントリーが毎週水曜日の週次更新で公開されると、同時にこのページにも追加されます。

またこのウイルスのタンパク質に関する解説記事を以下の「今月の分子」ページに掲載しています。

「全エントリー」のタブでは,同じ著者によるグループ登録のエントリーも全て区別し,すべてのPDB IDを省略せず表示しています。 「代表構造」タブには最も分解能の高い代表構造のみを表示しており,アミノ酸配列が100%同じPDBエントリーはリガンドが異なるものも含め除外してあります。 「最新のエントリー」のタブは,今週公開された最も新しいエントリーです。


作成日: 2020-09-03 (最終更新日: more than 1 year ago)2022-09-02
8U3O
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BU of 8u3o by Molmil
SARS-CoV-2 Main Protease A173V in complex with CDD-1819
分子名称: (2P)-2-(isoquinolin-4-yl)-1-[(1s,3R)-3-(methylcarbamoyl)cyclobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide, ORF1a polyprotein
著者Nnabuife, C, Palzkill, T.
登録日2023-09-08
公開日2024-09-18
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献SARS-CoV-2 Main Protease A173V in complex with CDD-1819
To Be Published
8ZBQ
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BU of 8zbq by Molmil
Local map of Omicron Subvariant JN.1 RBD with ACE2
分子名称: Angiotensin-converting enzyme 2, Spike protein S2'
著者Yan, R.H, Yang, H.N.
登録日2024-04-27
公開日2024-09-18
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants.
Nat Commun, 15, 2024
9ATO
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BU of 9ato by Molmil
XBB.1.5 spike/Nanosota-3C complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-3C, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-02-27
公開日2024-09-18
最終更新日2025-04-02
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structure-guided in vitro evolution of nanobodies targeting new viral variants.
Plos Pathog., 20, 2024
8WFH
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BU of 8wfh by Molmil
Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1
分子名称: D1 scFv, Spike protein S1
著者Terekhov, S.S, Mokrushina, Y.A, Zhang, M, Zhang, N, Gabibov, A, Guo, Y.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-11-27
実験手法X-RAY DIFFRACTION (2.72 Å)
主引用文献Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1
To Be Published
8WFM
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BU of 8wfm by Molmil
Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11
分子名称: Spike protein S1, T11 scFv
著者Terekhov, S.S, Mokrushina, Y.A, Zhang, M, Zhang, N, Gabibov, A, Guo, Y.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-11-27
実験手法X-RAY DIFFRACTION (2.99 Å)
主引用文献Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11
To Be Published
9DN4
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BU of 9dn4 by Molmil
Crystal structure of a SARS-CoV-2 20-mer RNA in complex with FAB BL3-6S97N
分子名称: CHLORIDE ION, FAB BL3-6S97N HEAVY CHAIN, FAB BL3-6S97N LIGHT CHAIN, ...
著者Lovell, S, Cooper, A, Battaile, K.P, Hegde, S, Wang, J.
登録日2024-09-16
公開日2024-09-25
最終更新日2025-07-02
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Mechanistic studies of small molecule ligands selective to RNA single G bulges.
Nucleic Acids Res., 53, 2025
8WKE
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BU of 8wke by Molmil
Sulfate-bound SARS-CoV-2 Nsp9
分子名称: Non-structural protein 9, SULFATE ION
著者Chen, P.J, Huang, H.Y, Hsiao, W.C, Huang, C.Y.
登録日2023-09-27
公開日2024-10-02
実験手法X-RAY DIFFRACTION (2.12 Å)
主引用文献Sulfate-bound SARS-CoV-2 Nsp9
To Be Published
8WSJ
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BU of 8wsj by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=6.5
分子名称: 3C-like proteinase nsp5
著者Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
登録日2023-10-17
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease, pH=6.5
To Be Published
8WSK
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BU of 8wsk by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=8.5
分子名称: 3C-like proteinase nsp5
著者Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
登録日2023-10-17
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease, pH=8.5
To Be Published
8K18
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BU of 8k18 by Molmil
Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
分子名称: Spike protein S1, ZCP4C9 heavy chain, ZCP4C9 light chain
著者Bingjie, T, Shangyu, D.
登録日2023-07-10
公開日2024-10-09
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.68 Å)
主引用文献Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
To Be Published
8K19
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BU of 8k19 by Molmil
Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
分子名称: Spike protein S1, ZCP3B4 heavy chain, ZCP3B4 light chain
著者Tang, B, Dang, S.
登録日2023-07-10
公開日2024-10-09
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.88 Å)
主引用文献Ultrapotent class I neutralizing antibodies post Omicron breakthrough infection overcome broad SARS-CoV-2 escape variants.
Ebiomedicine, 108, 2024
8WXL
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BU of 8wxl by Molmil
Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2023-10-30
公開日2024-10-09
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (2.59 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XUX
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BU of 8xux by Molmil
Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3.22 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XV0
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BU of 8xv0 by Molmil
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (up state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XVM
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BU of 8xvm by Molmil
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (3-up state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-15
公開日2024-10-09
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (2.77 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
9IU1
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BU of 9iu1 by Molmil
Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-07-20
公開日2024-10-09
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (4.3 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8WPW
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BU of 8wpw by Molmil
Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CB6 fab mutant heavy chain, CB6 fab mutant light chain, ...
著者Su, C, Qi, J.X, Gao, G.F.
登録日2023-10-10
公開日2024-10-16
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.49 Å)
主引用文献An improved design method enables the ineffective etesevimab broadly and efficiently against SARS-CoV-2 Omicron subvariants
To Be Published
8WPY
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BU of 8wpy by Molmil
Cryo-EM structure of SARS-CoV-2 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
分子名称: CB6 fab mutant heavy chain, CB6 fab mutant light chain, S304 fab heavy chain, ...
著者Su, C, Qi, J.X, Gao, G.F.
登録日2023-10-10
公開日2024-10-16
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.02 Å)
主引用文献An improved design method enables the ineffective etesevimab broadly and efficiently against SARS-CoV-2 Omicron subvariants
To Be Published
9ATM
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BU of 9atm by Molmil
SARS-CoV-2 EG.5 RBD bound to the VIR-7229 and the S2H97 Fab fragments
分子名称: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Rietz, T, Park, Y.J, Errico, J, Czudnochowski, N, Nix, J.C, Corti, D, Snell, G, Marco, A.D, Pinto, D, Cameroni, E, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
登録日2024-02-27
公開日2024-10-16
最終更新日2024-12-25
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9AU1
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BU of 9au1 by Molmil
SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ...
著者Rietz, T, Park, Y.J, Errico, J, Czudnochowski, N, Nix, J.C, Corti, D, Snell, G, Marco, A.D, Pinto, D, Cameroni, E, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D, Structural Genomics Consortium (SGC)
登録日2024-02-27
公開日2024-10-16
最終更新日2024-12-25
実験手法X-RAY DIFFRACTION (2.41 Å)
主引用文献A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9AU2
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BU of 9au2 by Molmil
VIR-7229 Fab fragment bound the BA.2.86 spike trimer (global refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
著者Tortorici, M.A, Park, Y.J, Veelser, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2024-02-28
公開日2024-10-16
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9CMN
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BU of 9cmn by Molmil
Room-temperature X-ray structure of SARS-CoV-2 main protease drug resistant mutant (E166A, L167F)
分子名称: 3C-like proteinase nsp5
著者Kovalevsky, A, Coates, L, Gerlits, O.
登録日2024-07-15
公開日2024-10-16
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors.
J.Med.Chem., 67, 2024
9GS4
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BU of 9gs4 by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571130
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
登録日2024-09-13
公開日2024-10-16
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8S6M
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BU of 8s6m by Molmil
SARS-CoV-2 BQ.1.1 RBD bound to the S2V29 and the S2H97 Fab fragments
分子名称: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Errico, J.M, Park, Y.J, Rietz, T, Czudnochowski, N, Nix, J.C, Cameroni, E, Corti, D, Snell, G, Marco, A.D, Pinto, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
登録日2024-02-28
公開日2024-10-23
最終更新日2024-12-25
実験手法X-RAY DIFFRACTION (1.67 Å)
主引用文献A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
8VIA
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BU of 8via by Molmil
Protective effect of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, PVI.V5-4 heavy chain, ...
著者Bajic, G.
登録日2024-01-03
公開日2024-10-23
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination.
Cell Rep, 43, 2024

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件を2025-07-09に公開中

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